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The Deubiquitinating Enzyme USP37 Regulates the Oncogenic Fusion Protein PLZF/RARA Stability

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The Deubiquitinating Enzyme USP37 Regulates the Oncogenic Fusion Protein PLZF/RARA Stability Oncogene (2012), 1–9 & 2012 Macmillan Publishers Limited All rights reserved 0950-9232/12 www.nature.com/onc ORIGINAL ARTICLE The deubiquitinating enzyme USP37 regulates the oncogenic fusion protein PLZF/RARA stability W-C Yang1,2,3 and H-M Shih1,2,3 Acute promyelocytic leukemia (APL) is predominantly characterized by chromosomal translocations between the retinoic acid receptor, alpha (RARA) gene and the promyelocytic leukemia (PML) or promyelocytic leukemia zinc finger (PLZF) gene. In APL cells with PML/ RARA fusions, arsenic trioxide and all-trans retinoic acid treatments specifically target the fusion protein for proteasome-dependent degradation, thereby promoting cellular differentiation and clinical remission of disease. In contrast, APL cells expressing PLZF/RARA fusion proteins are largely resistant to similar treatments and prognosis for patients with this translocation is poor. Understanding the molecular mechanisms regulating PLZF/RARA protein stability would provide novel therapeutic targets for PLZF/RARA-associated APL. Toward this end, we have performed an RNAi-based screen to identify factors affecting PLZF/RARA stability. Among the factors identified was the ubiquitin-specific peptidase 37 (USP37). We showed that USP37 interacted with PLZF/RARA through the PLZF moiety and sustained PLZF/RARA steady state levels. Domain mapping study revealed that N-terminal domain of USP37 is required for the PLZF/RARA interaction and protein regulation. Furthermore, overexpression or depletion of USP37 caused an increase or decrease of PLZF/RARA protein half-life, correlating with down- or upregulation of PLZF/RARA poly-ubiquitination, respectively. By PLZF/RARA- transduced primary mouse hematopoietic progenitor cells, we demonstrated that Usp37 knockdown alleviated PLZF/RARA-mediated target gene suppression and cell transformation potential. Altogether, our findings of USP37-modulating PLZF/RARA stability and cell transformation suggest that USP37 is a potential therapeutic target for PLZF/RARA-associated APL. Oncogene advance online publication, 3 December 2012; doi:10.1038/onc.2012.537 Keywords: acute promyelocytic leukemia; deubiquitinating enzyme; USP37; PLZF; RARA INTRODUCTION Ubiquitination-proteasome-dependent proteolysis is a major 9 Acute promyelocytic leukemia (APL) is a rare disease characterized cellular pathway to control protein stability. Protein ubiqui- by the chromosomal translocations between the retinoic acid tination is a cascade reaction involving a group of specialized receptor, alpha (RARA) gene and its counterpart gene (X), resulting protein family called ubiquitin-activating enzyme E1, ubiquitin- in an aberrant fusion protein X-RARA, such as promyelocytic conjugating enzyme E2 and ubiquitin ligase E3. Conversely, this leukemia (PML)/RARA, promyelocytic leukemia zinc finger (PLZF)/ biological process can be reversed by deubiquitinating enzymes RARA, NPM/RARA, NuMA/RARA or STAT5b/RARA.1 In APL patients, (DUBs), which are proteases functioning by removing conjugated abnormal accumulation of undifferentiated promyelocytes is ubiquitin from substrates.10 In general, the ubiquitination level of generally observed in bone marrow, which is because of the a substrate is regulated by its associated E3 ubiquitin ligase blockage of cellular differentiation in myeloid lineage. Such and/or DUB, correlating with the regulation of substrate protein differentiation arrest is in part resulted from dysregulation of stability. Thus, E3 ubiquitin ligases and DUBs are considered as key transcriptional regulators such as CEBPa involved in myeloid potential targets for regulation of disease-associated protein differentiation by those X-RARA proteins.2,3 All-trans retinoic acid stability. By sequence comparison, about 100 DUB genes have (ATRA) treatment has been introduced for APL cells expressing been annotated in human genome.11,12 According to the protein those X-RARA fusions by promoting cellular differentiation and secondary structure of DUBs, these DUBs can be divided into five clinical remission of disease. Although APL cells expressing PLZF/ different subclasses, including four cysteine protease DUBs, RARA fusion are responsive to ATRA treatment for cell ubiquitin-specific protease (USP), Machado–Joseph disease pro- differentiation,4 PLZF/RARA-associated APL patients, distinct tease, Otubain protease (OTU), and ubiquitin C-terminal hydrolase, from other X-RARA types of APL patients, are resistant to ATRA and one metalloprotease DUB, JAB1/MPN/Mov34 metalloen- therapy.2 In addition to ATRA, arsenic trioxide has been zyme.12 By global proteomic approach, DUBs have been shown successfully used for clinical remission of APL patients carrying to participate in several cellular functions, including DNA damage PML/RARA fusions specifically.5,6 Arsenic trioxide treatment and repair, protein quality control and degradation, RNA specifically triggers the poly-SUMO chain formation of PML/ transcription and processing, and signal transductions.13 RARA, subsequently targeting PML/RARA fusions for poly- In present study, we have identified USP37-regulating PLZF/ ubiquitination and protein degradation.7,8 Such therapy- RARA protein stability by RNAi screening. USP37 could bind and triggered degradation of an oncoprotein could potentially serve deubiquitinate PLZF/RARA fusion, thereby enhancing PLZF/RARA as a general strategy to eliminate cancer cells. protein stability. Knockdown of Usp37 in mouse primary 1Molecular Medicine Program, Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei, Taiwan; 2Institute of Biochemistry and Molecular Biology, School of Life Science, National Yang-Ming University, Taipei, Taiwan and 3Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan. Correspondence: Professor H-M Shih, Institute of Biomedical Sciences, Academia Sinica, 128, Sec.2, Academia Rd., Nankang 115, Taipei, Taiwan. E-mail: [email protected] Received 30 May 2012; revised 3 October 2012; accepted 19 October 2012 USP37 deubiquitinates PLZF/RARA W-C Yang and H-M Shih 2 hematopoietic progenitor cells could attenuate PLZF/RARA- RARA/PLZF (Figure 2b), neither affected the protein level of mediated target gene suppression and cell transformation. These another abnormal fusion protein PML/RARA (Figure 2c). In results suggest that USP37 is an important factor in modulating contrast, expression of USP29 but not OTUD7B could increase oncogenesis induced by PLZF/RARA fusion in APL cells. PML/RARA protein level (Supplementary Figure S2c). These data suggest that USP37 may stabilize PLZF/RARA through the PLZF moiety, whereas USP29 may exert similar function via the RARA RESULTS moiety in cells. The nature of OTUD7B affecting the levels of PLZF/ RNAi screening identifies DUBs modulating PLZF/RARA protein RARA and RARA, but not the levels of PLZF and PML/RARA, is level currently unclear. We further substantiated the specificity of To monitor PLZF/RARA protein level in cells, we have generated USP37 targeting to the PLZF moiety by USP37 knockdown the U937 myeloid leukemia cell line carrying a cassette in which experiments. USP37 depletion reduced endogenous PLZF level both EGFP-fused PLZF/RARA and tRFP driven by an internal but not RARA level in HL60 cells (Figure 2d, left panel). In contrast, ribosome entry site were induced to express by addition of USP37 knockdown failed to significantly alter the protein level of doxycycline (Figure 1a). In this screening, EGFP intensity was endogenous PML/RARA and RARA in NB4 cells (right panel), a cell measured to represent PLZF/RARA protein expression level, while line derived from long-term cultures of human APL. Altogether, tRFP intensity was served as an internal control for the normal- the findings that USP37 conferred the specific regulation on PLZF/ ization of EGFP intensity. Lentiviruses carrying shRNA clones RARA, but not on PML/RARA level, led us to focus on the study of targeting to 83 human DUBs were used to infect U937 cells USP37 in regulating PLZF/RARA. (Supplementary Table S1). Following the puromycin selection for We next examined whether USP37-regulated PLZF/RARA cells expressing shRNA and doxycycline induction for expression protein level is relevant to its protease catalytic activity. USP37 of the PLZF/RARA cassette, the cells were subjected to 96-well catalytically inactive mutant, converting Cys350 to Ala (CA), was flow cytometry analysis for measuring both EGFP and tRFP generated to examine for PLZF/RARA regulation. As expected, the intensities (Figure 1b). The P-values were calculated and adjusted USP37 CA mutant was impaired to enhance PLZF/RARA protein on the basis of comparing EGFP/tRFP ratio between knockdown level as compared with WT (Figure 2e), indicating the importance and control clones. To avoid the possible off-target effects of of USP37 catalytic activity for PLZF/RARA regulation. Noted certain shRNA clones, DUB targeted by at least three shRNA clones that overexpression of USP37 CA mutant rendered USP37 showing significant effect (P-valueo0.0001) on decreasing multiple-band shifts. These slowly migrating bands were K48- EGFP/tRFP ratio was chosen as a candidate for further study. linkage ubiquitinated USP37 proteins, as evidenced by western Eight candidate DUBs, including MPND, OTUD5, OTUD6A, blot analysis with antibodies against specific ubiquitin linkage OTUD6B, OTUD7B, USP2, USP29 and USP37 were initially identified (Supplementary Figure S3). In addition, PLZF/RARA mRNA (Supplementary Table S2). To further validate whether level was not altered by USP37
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